DGRPool

GWAS results were computed on dm3 genome.

If you want to make an independent analysis with DGRP2 or PLINK2, you can find here prepared input files for this phenotype: DGRP2 results PLINK2 results

Full results

Phenotype distribution and association to known covariates

Shapiro-Wilk test of normality (p-value=9.156e^-16)
Null Hypothesis is rejected (p<=0.05).
Interpretation: NOT NORMAL distribution of this phenotype

We tested for association of this phenotype with 6 known covariates Huang et al., 2014 using both ANOVA and Kruskal-Wallis association tests.

ANOVA test
No significant result.

Kruskal-Wallis test
No significant result.

PNG PDF

QQplot

PNG PDF

Manhattan plot

GWAS results

1685 significant hits at p-value < 0.001. The 1000 top results are displayed in the table below.

We performed a gene enrichment calculation (Fisher's exact test) of all GWAS-associated genes at p < 0.001. Genesets were taken from two database: the Gene Ontology (GO) and the FlyBase phenotypes. GO enrichment FlyBase phenotype enrichment

Variant impact HIGH MODERATE LOW MODIFIER

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Chromosome	Position	ID	Reference	Variant	p-value	FDR_BH	Transcript annotation	Binding site annotation
3L	453468	3L_453468_SNP [dm3] 3L_453468_SNP [dm6]	T	C	1.576e^-6	1	SYNONYMOUS_CODING klar UTR_5_PRIME klar INTRON klar
2R	10588859	2R_10588859_SNP [dm3] 2R_14701354_SNP [dm6]	C	T	2.510e^-6	1	INTRON mspo
X	16086178	X_16086178_SNP [dm3] X_16192145_SNP [dm6]	T	C	2.919e^-6	1	UPSTREAM mir-985 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_HSA
X	15996210	X_15996210_SNP [dm3] X_16102177_SNP [dm6]	C	T	4.298e^-6	1	INTRON CG42354 & 1 other	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
2L	17798976	2L_17798976_SNP [dm3] 2L_17798976_SNP [dm6]	A	T	6.341e^-6	1	SYNONYMOUS_CODING CadN2	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
3L	5503672	3L_5503672_SNP [dm3] 3L_5510572_SNP [dm6]	G	T	6.880e^-6	1	INTRON CG34342
3L	8466935	3L_8466935_SNP [dm3] 3L_8473835_SNP [dm6]	C	G	6.928e^-6	1	SYNONYMOUS_CODING CG43163	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	9557704	2L_9557704_SNP [dm3] 2L_9557704_SNP [dm6]	G	A	7.247e^-6	1	INTRON jp
3L	453564	3L_453564_DEL [dm3] 3L_453564_DEL [dm6]	TGTT	CA	7.839e^-6	1	INTRON klar
3L	5244152	3L_5244152_SNP [dm3] 3L_5251052_SNP [dm6]	C	T	8.065e^-6	1	INTRON shep
2L	1033533	2L_1033533_SNP [dm3] 2L_1033533_SNP [dm6]	G	C	8.288e^-6	1	INTRON IA-2
2R	16478336	2R_16478336_SNP [dm3] 2R_20590831_SNP [dm6]	T	C	9.367e^-6	1	INTRON bl
3L	8466923	3L_8466923_SNP [dm3] 3L_8473823_SNP [dm6]	A	G	9.914e^-6	1	SYNONYMOUS_CODING CG43163	TF binding site mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens
2L	5277388	2L_5277388_SNP [dm3] 2L_5277388_SNP [dm6]	T	G	9.962e^-6	1	UPSTREAM Bsg25D INTRON Bsg25D	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2L	13244603	2L_13244603_SNP [dm3] 2L_13244603_SNP [dm6]	G	A	1.147e^-5	1	UPSTREAM snRNA:U5:34A & 1 other EXON CR45330	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_disco mE1_TFBS_HSA
2R	13701189	2R_13701189_SNP [dm3] 2R_17813684_SNP [dm6]	C	T	1.258e^-5	1	UPSTREAM grh INTRON grh	TF binding site BDTNP1_TFBS_sna
2R	13701174	2R_13701174_INS [dm3] 2R_17813669_INS [dm6]	A	AA	1.348e^-5	1	UPSTREAM grh INTRON grh	TF binding site BDTNP1_TFBS_sna
2L	7048062	2L_7048062_SNP [dm3] 2L_7048062_SNP [dm6]	G	T	1.356e^-5	1	INTRON milt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_twi mE1_TFBS_cad
3L	5496593	3L_5496593_SNP [dm3] 3L_5503493_SNP [dm6]	A	C	1.426e^-5	1	DOWNSTREAM CG34342 INTERGENIC
2R	18024362	2R_18024362_SNP [dm3] 2R_22136857_SNP [dm6]	T	G	1.439e^-5	1	UPSTREAM a INTERGENIC	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA mE1_TFBS_Trl
3L	5244413	3L_5244413_SNP [dm3] 3L_5251313_SNP [dm6]	C	G	1.590e^-5	1	INTRON shep	TF binding site mE1_TFBS_HSA mE1_TFBS_inv
3L	12165479	3L_12165479_SNP [dm3] 3L_12172379_SNP [dm6]	G	T	1.605e^-5	1	INTRON Rh7
3L	8822769	3L_8822769_SNP [dm3] 3L_8829669_SNP [dm6]	G	C	1.703e^-5	1	INTRON dally	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_cnc mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
2L	5277650	2L_5277650_SNP [dm3] 2L_5277650_SNP [dm6]	T	A	1.770e^-5	1	UPSTREAM Bsg25D INTRON Bsg25D	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	12292488	2R_12292488_SNP [dm3] 2R_16404983_SNP [dm6]	C	T	1.804e^-5	1	INTRON Sema-2b
3L	5897461	3L_5897461_SNP [dm3] 3L_5904361_SNP [dm6]	T	G	1.809e^-5	1	UTR_3_PRIME CG10486 UPSTREAM CG32413
3L	1399465	3L_1399465_SNP [dm3] 3L_1399465_SNP [dm6]	G	A	1.850e^-5	1	SPLICE_SITE_REGION CG32320 DOWNSTREAM tRNA:CR32324 INTRON Ptp61F & 1 other	TF binding site mE1_TFBS_sens
3L	5244165	3L_5244165_SNP [dm3] 3L_5251065_SNP [dm6]	A	G	1.940e^-5	1	INTRON shep	TF binding site mE1_TFBS_inv
2L	13142094	2L_13142094_SNP [dm3] 2L_13142094_SNP [dm6]	T	G	1.960e^-5	1	DOWNSTREAM CG9928 INTERGENIC
3L	453730	3L_453730_SNP [dm3] 3L_453730_SNP [dm6]	A	T	1.970e^-5	1	INTRON klar
2L	5277617	2L_5277617_SNP [dm3] 2L_5277617_SNP [dm6]	T	C	2.048e^-5	1	UPSTREAM Bsg25D INTRON Bsg25D	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
3R	16804318	3R_16804318_SNP [dm3] 3R_20978596_SNP [dm6]	T	A	2.069e^-5	1	UTR_5_PRIME Calx INTRON Calx	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_twi mE1_TFBS_HSA
X	12042611	X_12042611_SNP [dm3] X_12148578_SNP [dm6]	T	G	2.142e^-5	1	INTRON Ten-a
3L	1499443	3L_1499443_SNP [dm3] 3L_1499443_SNP [dm6]	T	C	2.143e^-5	1	UTR_5_PRIME pUf68 UPSTREAM scaRNA:MeU2-48 INTRON pUf68	TF binding site mE1_TFBS_cad
2R	16478353	2R_16478353_SNP [dm3] 2R_20590848_SNP [dm6]	A	C	2.293e^-5	1	INTRON bl
3L	20842581	3L_20842581_INS [dm3] 3L_20849481_INS [dm6]	GG	TCA	2.311e^-5	1	INTRON CG32432
X	15666730	X_15666730_SNP [dm3] X_15772697_SNP [dm6]	C	A	2.572e^-5	1	NON_SYNONYMOUS_CODING CG33172 UPSTREAM CG43672
2L	9553187	2L_9553187_SNP [dm3] 2L_9553187_SNP [dm6]	A	G	2.608e^-5	1	SYNONYMOUS_CODING jp	TF binding site BDTNP1_TFBS_sna mE1_TFBS_cad mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8470830	3L_8470830_SNP [dm3] 3L_8477730_SNP [dm6]	C	G	2.696e^-5	1	SYNONYMOUS_CODING CG43163	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
2L	13142087	2L_13142087_SNP [dm3] 2L_13142087_SNP [dm6]	G	T	2.731e^-5	1	DOWNSTREAM CG9928 INTERGENIC
3L	5496594	3L_5496594_SNP [dm3] 3L_5503494_SNP [dm6]	A	T	2.751e^-5	1	DOWNSTREAM CG34342 INTERGENIC
2L	1033550	2L_1033550_SNP [dm3] 2L_1033550_SNP [dm6]	G	A	2.756e^-5	1	INTRON IA-2
3L	8315384	3L_8315384_SNP [dm3] 3L_8322284_SNP [dm6]	T	A	2.771e^-5	1	DOWNSTREAM CG13670 INTERGENIC
3L	2901686	3L_2901686_SNP [dm3] 3L_2901686_SNP [dm6]	C	T	2.837e^-5	1	INTRON Shab
2R	14389175	2R_14389175_SNP [dm3] 2R_18501670_SNP [dm6]	A	C	2.849e^-5	1	INTERGENIC
3L	9517398	3L_9517398_SNP [dm3] 3L_9524298_SNP [dm6]	A	T	2.877e^-5	1	INTRON CG33700
3L	12514878	3L_12514878_SNP [dm3] 3L_12521778_SNP [dm6]	G	C	2.882e^-5	1	SYNONYMOUS_CODING Gcn5 DOWNSTREAM tral	TF binding site mE1_TFBS_cad
2L	16987595	2L_16987595_DEL [dm3] 2L_16987595_DEL [dm6]	ATAGATAATAGATAGATAGA...	A	2.894e^-5	1	INTRON beat-IIIb
X	17838388	X_17838388_SNP [dm3] X_17944355_SNP [dm6]	G	A	2.964e^-5	1	INTRON Sh
X	16721094	X_16721094_SNP [dm3] X_16827061_SNP [dm6]	A	T	3.041e^-5	1	UTR_3_PRIME CG13004 DOWNSTREAM CG13004 & 1 other
2L	17461320	2L_17461320_INS [dm3] 2L_17461320_INS [dm6]	A	AGTTAACA	3.227e^-5	1	UTR_3_PRIME BicD DOWNSTREAM BicD
2L	1033544	2L_1033544_SNP [dm3] 2L_1033544_SNP [dm6]	G	A	3.288e^-5	1	INTRON IA-2
2L	2312401	2L_2312401_SNP [dm3] 2L_2312401_SNP [dm6]	T	A	3.311e^-5	1	INTRON CG9967 & 1 other
X	12042596	X_12042596_SNP [dm3] X_12148563_SNP [dm6]	A	T	3.374e^-5	1	INTRON Ten-a
X	12042592	X_12042592_SNP [dm3] X_12148559_SNP [dm6]	T	G	3.378e^-5	1	INTRON Ten-a
2L	5277357	2L_5277357_SNP [dm3] 2L_5277357_SNP [dm6]	T	A	3.399e^-5	1	UPSTREAM Bsg25D INTRON Bsg25D	regulatory region REDfly_CRMs TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA
2R	10588889	2R_10588889_SNP [dm3] 2R_14701384_SNP [dm6]	T	A	3.519e^-5	1	INTRON mspo
2R	14522653	2R_14522653_DEL [dm3] 2R_18635148_DEL [dm6]	TGCTT	T	3.535e^-5	1	INTRON CG30122	TF binding site BDTNP1_TFBS_dl mE1_TFBS_HSA
3L	18304965	3L_18304965_SNP [dm3] 3L_18311865_SNP [dm6]	G	A	3.549e^-5	1	INTERGENIC
2R	5842223	2R_5842223_SNP [dm3] 2R_9954718_SNP [dm6]	A	T	3.645e^-5	1	INTRON Mef2	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_Med mE1_TFBS_cad mE1_TFBS_D mE1_TFBS_HSA mE1_TFBS_Trl
2R	6807081	2R_6807081_SNP [dm3] 2R_10919576_SNP [dm6]	G	A	3.705e^-5	1	INTERGENIC
3L	13918590	3L_13918590_SNP [dm3] 3L_13925490_SNP [dm6]	T	A	3.835e^-5	1	UPSTREAM Rgl DOWNSTREAM CG8833 INTERGENIC	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_sna BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_sens mE1_TFBS_Trl
3L	20338355	3L_20338355_SNP [dm3] 3L_20345255_SNP [dm6]	G	A	3.859e^-5	1	DOWNSTREAM Spn77Bc & 1 other EXON CR45385
X	14035079	X_14035079_SNP [dm3] X_14141046_SNP [dm6]	A	T	3.993e^-5	1	UPSTREAM CR44658 INTERGENIC
X	17838358	X_17838358_SNP [dm3] X_17944325_SNP [dm6]	C	A	4.091e^-5	1	INTRON Sh
3L	14272908	3L_14272908_SNP [dm3] 3L_14279808_SNP [dm6]	G	A	4.123e^-5	1	INTRON fz
X	12253322	X_12253322_DEL [dm3] X_12359289_DEL [dm6]	CTTAATAAGCGAAGAGTCCT...	C	4.186e^-5	1	INTERGENIC
3R	19068321	3R_19068321_SNP [dm3] 3R_23242599_SNP [dm6]	A	G	4.223e^-5	1	INTRON CG4467
X	8818305	X_8818305_SNP [dm3] X_8924272_SNP [dm6]	A	G	4.243e^-5	1	SYNONYMOUS_CODING CG43255 UPSTREAM CG12661 & 1 other INTRON rdgA	TF binding site BDTNP1_TFBS_dl mE1_TFBS_Trl
3L	18129846	3L_18129846_SNP [dm3] 3L_18136746_SNP [dm6]	A	T	4.272e^-5	1	UPSTREAM CR44669 INTERGENIC
3L	12165663	3L_12165663_SNP [dm3] 3L_12172563_SNP [dm6]	A	G	4.278e^-5	1	INTRON Rh7
2L	4842954	2L_4842954_SNP [dm3] 2L_4842954_SNP [dm6]	C	T	4.309e^-5	1	UTR_3_PRIME mxt INTRON mxt
2L	17166055	2L_17166055_SNP [dm3] 2L_17166055_SNP [dm6]	C	T	4.415e^-5	1	INTRON beat-IIIa & 1 other
2L	12957256	2L_12957256_SNP [dm3] 2L_12957256_SNP [dm6]	T	C	4.446e^-5	1	INTERGENIC
2L	2651016	2L_2651016_SNP [dm3] 2L_2651016_SNP [dm6]	C	T	4.464e^-5	1	NON_SYNONYMOUS_CODING CG33125
2R	10588879	2R_10588879_SNP [dm3] 2R_14701374_SNP [dm6]	C	T	4.479e^-5	1	INTRON mspo
3L	9283273	3L_9283273_DEL [dm3] 3L_9290173_DEL [dm6]	AATA	A	4.483e^-5	1	INTERGENIC
2R	10588870	2R_10588870_SNP [dm3] 2R_14701365_SNP [dm6]	T	C	4.690e^-5	1	INTRON mspo
3L	15620494	3L_15620494_SNP [dm3] 3L_15627394_SNP [dm6]	A	C	4.913e^-5	1	INTRON comm3
2L	7048716	2L_7048716_SNP [dm3] 2L_7048716_SNP [dm6]	G	A	4.936e^-5	1	UPSTREAM milt INTRON milt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_HSA mE1_TFBS_Trl
3L	8470746	3L_8470746_SNP [dm3] 3L_8477646_SNP [dm6]	T	A	4.952e^-5	1	SYNONYMOUS_CODING CG43163	TF binding site mE1_TFBS_cad mE1_TFBS_chinmo
3R	16652099	3R_16652099_SNP [dm3] 3R_20826377_SNP [dm6]	T	C	5.030e^-5	1	UPSTREAM CR44047 INTRON AdSS	TF binding site mE1_TFBS_cad
X	16234624	X_16234624_SNP [dm3] X_16340591_SNP [dm6]	G	C	5.089e^-5	1	UTR_3_PRIME Dsp1 DOWNSTREAM Dsp1
2R	11317729	2R_11317729_SNP [dm3] 2R_15430224_SNP [dm6]	A	T	5.090e^-5	1	INTRON CG43729
2R	5335362	2R_5335362_SNP [dm3] 2R_9447857_SNP [dm6]	G	C	5.144e^-5	1	INTRON Camta	TF binding site mE1_TFBS_chinmo mE1_TFBS_HSA
3L	8461754	3L_8461754_SNP [dm3] 3L_8468654_SNP [dm6]	G	A	5.288e^-5	1	SYNONYMOUS_CODING Gug	TF binding site mE1_TFBS_cad
2R	16476830	2R_16476830_SNP [dm3] 2R_20589325_SNP [dm6]	T	A	5.319e^-5	1	INTRON bl	TF binding site BDTNP1_TFBS_dl
2L	17166079	2L_17166079_SNP [dm3] 2L_17166079_SNP [dm6]	A	G	5.378e^-5	1	INTRON beat-IIIa & 1 other
3L	8823220	3L_8823220_SNP [dm3] 3L_8830120_SNP [dm6]	C	T	5.388e^-5	1	INTRON dally	TF binding site BDTNP1_TFBS_da BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_Med BDTNP1_TFBS_prd BDTNP1_TFBS_slp1 BDTNP1_TFBS_sna BDTNP1_TFBS_tll BDTNP1_TFBS_twi mE1_TFBS_cad mE1_TFBS_eve mE1_TFBS_HSA mE1_TFBS_Trl
2L	19693194	2L_19693194_SNP [dm3] 2L_19693194_SNP [dm6]	A	G	5.482e^-5	1	INTRON Lar
2L	12133554	2L_12133554_SNP [dm3] 2L_12133554_SNP [dm6]	G	C	5.570e^-5	1	UPSTREAM rho-6 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3R	18749746	3R_18749746_SNP [dm3] 3R_22924024_SNP [dm6]	T	C	5.571e^-5	1	SYNONYMOUS_CODING CG6660 INTRON klg	TF binding site mE1_TFBS_chinmo
2L	7048487	2L_7048487_INS [dm3] 2L_7048487_INS [dm6]	T	TTTTGGATATGGTAAT...	5.618e^-5	1	UPSTREAM milt INTRON milt	TF binding site BDTNP1_TFBS_bcd BDTNP1_TFBS_dl BDTNP1_TFBS_gt BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_shn BDTNP1_TFBS_twi mE1_TFBS_cad
3L	7990775	3L_7990775_SNP [dm3] 3L_7997675_SNP [dm6]	C	T	5.632e^-5	1	INTRON nmo	TF binding site BDTNP1_TFBS_dl BDTNP1_TFBS_hb BDTNP1_TFBS_Med BDTNP1_TFBS_prd mE1_TFBS_HSA
2L	12133536	2L_12133536_SNP [dm3] 2L_12133536_SNP [dm6]	G	A	5.632e^-5	1	UPSTREAM rho-6 INTERGENIC	TF binding site BDTNP1_TFBS_twi mE1_TFBS_bab1 mE1_TFBS_HSA
3L	453789	3L_453789_SNP [dm3] 3L_453789_SNP [dm6]	T	G	5.669e^-5	1	INTRON klar
3L	453306	3L_453306_SNP [dm3] 3L_453306_SNP [dm6]	C	A	5.698e^-5	1	SYNONYMOUS_CODING klar UTR_5_PRIME klar INTRON klar
2R	16478272	2R_16478272_SNP [dm3] 2R_20590767_SNP [dm6]	C	A	5.739e^-5	1	INTRON bl
3L	9282082	3L_9282082_SNP [dm3] 3L_9288982_SNP [dm6]	G	A	5.793e^-5	1	DOWNSTREAM GluRIB INTERGENIC
3L	12165653	3L_12165653_SNP [dm3] 3L_12172553_SNP [dm6]	T	C	5.872e^-5	1	INTRON Rh7

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By genomic position
Variant impact
Gene name

Sample.size Experience 5 phenotype

Phenotype distribution and association to known covariates

QQplot

Manhattan plot

GWAS results